Commits for hiram

v323_preview to v323_preview2 (2015-09-21 to 2015-09-28) v323

• lastz run to danRer10 for user refs #15476
  
  • src/hg/makeDb/doc/mm10.txt - lines changed 62, context: html, text, full: html, text
• capture scripts in use as of today 2015-09-24 refs #16078
  
  • src/hg/utils/automation/genbank/agpToBbi.sh - lines changed 57, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/buildStats.pl - lines changed 84, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/compositeAgp.pl - lines changed 53, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/compositeFasta.pl - lines changed 69, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/gatewayPage.pl - lines changed 205, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiToUcsc.sh - lines changed 397, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/noStructureAgp.pl - lines changed 53, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/noStructureFasta.pl - lines changed 49, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/rmsk.sh - lines changed 86, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/rsync.sh - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/trackDb.sh - lines changed 196, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/unlocalizedAgp.pl - lines changed 59, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/unlocalizedFasta.pl - lines changed 65, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/unplacedAgp.pl - lines changed 35, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/unplacedFasta.pl - lines changed 58, context: html, text, full: html, text
• capture scripts in use as of today 2015-09-24 refs #16078
  
  • src/hg/utils/automation/genbank/idFromAsmRpt.pl - lines changed 100, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/idScan.sh - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/taxId.comName.tab - lines changed 10157, context: html, text, full: html, text
• capture scripts in use as of today 2015-09-24 refs #16078
  
  • src/hg/utils/automation/genbank/checksOK.sh - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/hubIndexNcbi.sh - lines changed 83, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiBacteria.sh - lines changed 149, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiBacteriaHtml.sh - lines changed 101, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiHtml.sh - lines changed 96, context: html, text, full: html, text
• capture scripts in use as of today 2015-09-24 refs #16078
  
  • src/hg/utils/automation/genbank/cronUpdate.sh - lines changed 58, context: html, text, full: html, text
• lastz run to danRer10 for user refs #15476
  
  • src/hg/makeDb/doc/rn6.txt - lines changed 61, context: html, text, full: html, text
• lastz run to danRer10 for user refs #15476
  
  • src/hg/makeDb/doc/hg19.txt - lines changed 70, context: html, text, full: html, text
• add chromSizes argument to allow working independently of UCSC standard directory hierarchy refs #16078
  
  • src/hg/utils/automation/doCpgIslands.pl - lines changed 7, context: html, text, full: html, text
• add chromSizes argument to allow working independently of UCSC standard directory hierarchy refs #16078
  
  • src/hg/utils/automation/doCpgIslands.pl - lines changed 2, context: html, text, full: html, text
• good to know chr name when error on start != prevEnd refs #16078
  
  • src/hg/gigAssembler/checkAgpAndFa/checkAgpAndFa.c - lines changed 2, context: html, text, full: html, text
• catching up to todays versions refs #16078
  
  • src/hg/utils/automation/genbank/alternatesAgp.pl - lines changed 41, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/assemblyDescription.pl - lines changed 83, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/cpg.sh - lines changed 63, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/gapDescription.pl - lines changed 81, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiToUcsc.sh - lines changed 100, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/rmsk.sh - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/trackDb.sh - lines changed 60, context: html, text, full: html, text
• correcting missing html bits refs #16078
  
  • src/hg/makeDb/trackDb/gc5Base.html - lines changed 13, context: html, text, full: html, text
• catching up with todays versions refs #16078
  
  • src/hg/utils/automation/genbank/cpgDescription.pl - lines changed 128, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/gc5Description.pl - lines changed 57, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiToUcsc.sh - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/rmskDescription.pl - lines changed 151, context: html, text, full: html, text
• v323 preview2 refs #16061
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text